Hi,
I do not know for input but if you look at the json galaxy format (not
the XML for a specific tool, the json format use to import/export a
workflow, which describe how tools follow), you could rename a file
with the "post_job_actions" tag.
The path for this tag in JSON tree is
{ « steps »: { « Step number » : {
Then, indicates the name you want for your file with
"RenameDatasetAction(...)", where (...) is the name of the original
file, define in the "output > name" tag ({ "steps": { "Step number" :
{ "tool": { "output" ).
Good luck.
-Regards,
Remy
2012/1/1 Peter Cock <p.j.a.c...@googlemail.com>
>
> On Sun, Jan 1, 2012 at 12:29 AM, Thon Deboer <thondeb...@me.com> wrote:
> > Thanks, but ${foo.name} did not work in the workflow to rename an output
> > file. It takes ${foo.name} to be a user provided parameter.
> >
> > ${foo.name} will definitely work in tool definitions, but that means I have
> > to change ALL the default tool names for all the tool in galaxy...Surely
> > there must be a way to rename an output file to the original input file in
> > the workflow step "Rename Dataset"?
>
> Sorry - I thought you were still talking about tool XML files.
>
> I'm not sure that there are any dynamic variables you can
> use in the workflow rename action to access properties
> of the tool that created the history item - but being able
> to use ${tool.param_name} or ${tool.input_file.name} or
> something like that could be quite powerful (where my
> made up syntax is $tool for the tool which created the
> history entry, and then dot and a tool parameter as
> named in the tool's XML). It would be possible even to
> expose those fields via the web interface, but for a
> first pass having an expert user type them in by hand
> would work.
>
> Interesting idea... I wonder what the Galaxy team
> think?
>
> Peter
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